AlphaFold3-based modeling uncovers the dynamic structural interface between full-length IAP antagonists and DIAP1 for apoptosis regulation in Drosophila

Abstract

Apoptosis in Drosophila is governed by caspases, inhibitor of apoptosis proteins (IAPs), and IAP antagonists. Using AlphaFold3, we modeled full-length 3D structures of the IAP antagonists Reaper, Hid, Grim, Sickle, and Jafrac2, as well as DIAP1 and dBruce, and their binary and higher-order complexes. We uncover a paradoxical role for the N-terminal methionine of Reaper in stabilizing Reaper/Hid complexes and inhibiting DIAP1 binding. Our models reveal that Reaper uniquely engages both BIR1 and BIR2 domains of DIAP1, guided by -helical residues in its backbone, while all other IAP antagonists preferentially target BIR2. Higher-order assemblies show how Reaper and Hid cooperatively engage DIAP1 and allosterically modulate its E3 ligase activity. We present the first full-length model of dBruce and its inhibitory interaction with Rpr. These findings provide a comprehensive structural framework for apoptosis regulation in Drosophila, and offer new insights into conserved mechanisms of caspase control and IAP antagonism across species.